Advanced Research in Molecular Genetics and Disease Mechanisms

1. 1A

2. -3s -2s -1s 0 +1s +2s +3s s = standard deviation from mean AT/RT CNS MD MGlio AT/RT Renal/Extrarenal Ncer PNET 1B 1C 1D 1E MD Mglio Rhab Ncer PNET M93119 INSM1 Insulinoma-associated 1 M30448 Casein kinase II beta subunit S82240 RhoE D80004 KIAA0182 gene D76435 Zic protein X83543 APXL Apical protein X62534 HMG2 High-mobility group M96739 NSCL-1 U26726 11 beta-hydroxysteroid dehydrogenase type II HG311-HT311 Ribosomal Protein L30 X86693 High endothelial venule M93426 PTPRZ Protein tyrosine phosphatase U48705 DDR gene X86809 Major astrocytic phosphoprotein PEA-15 U45955 Neuronal membrane glycoprotein M6b U53204 Plectin (PLEC1) X13916 LDL-receptor related protein D87258 Serin protease with IGF-binding motif Z31560 SOX2 SRY (sex determining region Y)-box 2 M32886 SRI Sorcin J04164 RPS3 Ribosomal protein S3 M12125 Skeletal beta-tropomyosin D29958 KIAA0116 gene D17400 PTS 6-pyruvoyltetrahydropterin synthase D83174 CBP1 Collagen-binding protein 1 D83735 Adult heart mRNA for neutral calponin D84454 UDP-galactose translocator L38969 Thrombospondin 3 (THBS3) U12465 RPS11 Ribosomal protein S11 D80005 KIAA0183 gene D87463 KIAA0273 gene U90902 Clone 23612 mRNA sequence D26070 Type 1 inositol 1,4,5-trisphosphate receptor X63578 Parvalbumin Z15108 PRKCZ Protein kinase C, zeta L35592 Germline mRNA sequence L10338 SCN1B Sodium channel L33243 PKD1 Polycystic kidney disease protein 1 L77864 Stat-like protein (Fe65) J04469 Mitochondrial creatine kinase (CKMT) M80397 POLD1 Polymerase (DNA directed), delta 1 X14830 CHRNB1 Cholinergic receptor, nicotinic, beta polypeptide 1 U97018 Echinoderm microtubule-associated protein homolog HuEMAP HG4178-HT4448 Af-17 K02882 IGHD gene X52228 MUC1 Mucin 1, transmembrane U22314 Neural-restrictive silencer factor D29675 Inducible nitric oxide synthase gene S82471 SSX3 M54951 Human atrial natriuretic factor gene

3. 2A Classic Desmoplastic HG1980-HT2023 Tubulin, Beta 2 U63842 NeuroD3 gene X67951 PAGA Proliferation-associated gene A X64330 ATP-citrate lyase J03241 TGFB3 Transforming growth factor, beta 3 U44839 Putative ubiquitin C-terminal hydrolase (UHX1) Z27113 H.Sapiens gene for RNA polymerase II subunit X12447 ALDOA Aldolase A U73328 DLX7 Distal-less homeobox 7 U59913 SMAD5 Z75190 Apolipoprotein E receptor 2 X15183 Human mRNA for 90-kDa heat-shock protein U61263 Acetolactate synthase homolog L07515 Human heterochromatin protein homologue (HP1) M34677 Human nested gene protein gene (coag. factorVIII) U40391 Serotonin N-acetyltransferase gene D16611 CPO Coproporphyrinogen oxidase L37127 RNA polymerase II U33839 No description available X81817 BAP31 X51804 Human PMI gene for a putative receptor protein Y09305 Protein kinase, Dyrk4 X14885 Transforming growth factor-beta 3 (TGF-beta 3) X57398 NME1 Non-metastatic cells 1 (NM23A) X02152 LDHA Lactate dehydrogenase A X64364 BSG Basigin U04806 FLT3/FLK2 ligand mRNA U52191 SMCY (H-Y) mRNA M35296 Tyrosine kinase arg gene D50840 Ceramide glucosyltransferase S69189 Peroxisomal acyl-coenzyme A oxidase L03785 MYL5 Myosin, light polypeptide 5 M82919 GABRB3 Gamma-aminobutyric acid (GABA) A receptor, beta 3 U65092 Melanocyte-specific gene 1 (msg1) S49592 Transcription factor E2F like protein D79994 KIAA0172 gene X95586 PSMB5 Proteasome subunit, beta type, 5 U79299 Human neuronal olfactomedin-related ER localized protein X71973 GPX4 Phospholipid hydroperoxide glutathione peroxidase U31342 Human nucleobindin gene U48437 Amyloid precursor-like protein 1 D86957 KIAA0202 gene HG2279-HT2375 Triosephosphate Isomerase Z19585 THBS4 Thrombospondin 4 M16405 Human m4 muscarinic acetylcholine receptor gene U32315 Syntaxin 3 U11701 LIM-homeobox domain protein (hLH-2) Y11251 Novel member of serine-arginine domain protein, SRrp129 U68018 Mad protein homolog (hMAD-2) M81181 ATP1B2 ATPase, Na+/K+ transporting, beta 2 polypeptide U58334 Bcl2, p53 binding protein Bbp/53BP2 L38490 ARF4L ADP-ribosylation factor 4-like M31328 GNB3 Guanine nucleotide binding protein M60626 FPR1 Formyl peptide receptor 1 M97815 CRABP2 Cellular retinoic acid-binding protein 2 J00116 COL2A1 Collagen, type II, alpha 1 U01824 Glutamate transporter Y00282 RPN2 Ribophorin II M65254 PPP2R1B Protein phosphatase 2 X64877 HFL1 H factor (complement)-like 1 D31885 KIAA0069 gene D87434 KIAA0247 gene Z35093 SURF1 Surfeit 1 Y08374 GP-39 cartilage protein gene Z54367 Plectin Z46632 PDE4C Phosphodiesterase 4C HG3517-HT3711 Alpha-1-Antitrypsin L42354 Clone 48ES4 mRNA fragment X15376 GABRG2 Gamma-aminobutyric acid (GABA) A receptor, gamma 2 X89059 Unknown protein expressed in macrophages Classic Desmoplastic IGF2 HG3543-HT3739 Insulin-Like Growth Factor 2 X53331 MGP Matrix protein gla X65724 NDP Norrie disease protein D14530 40S Ribosomal protein S23 Y00757 SGNE1 Secretory granule, neuroendocrine protein 1 U25789 Ribosomal protein L21 L27560 Insulin-like growth factor binding protein 5 (IGFBP5) X83543 APXL Apical protein (Xenopus laevis-like) X52966 RPL35A Ribosomal protein L35a L06797 Human (clone L5) orphan G protein-coupled receptor M14745 BCL2 B HG3431-HT3616 Decorin D79205 Ribosomal protein L39 D82345 NB thymosin beta D38549 KIAA0068 gene U14972 Ribosomal protein S10 X59841 PBX3 J03242 IGF2 Insulin-like growth factor 2 (somatomedin A) HG3214-HT3391 Metallopanstimulin 1 X06617 RPS11 Ribosomal protein S11 J02611 APOD Apolipoprotein D X16064 Human mRNA for translationally controlled tumor protein Z74616 COL1A2 Collagen, type I, alpha-2 L40386 DP2 (Humdp2) X04741 Human mRNA for protein gene product (PGP) M55210 LAMC1 Laminin, gamma 1 M96739 NSCL-1 U73304 CB1 cannabinoid receptor (CNR1) gene M65292 HFL1 H factor (complement)-like 1 HG311-HT311 Ribosomal Protein L30 M83233 TCF12 Transcription factor 12 U07919 ALDH6 Aldehyde dehydrogenase 6 X57959 RPL17 Ribosomal protein L7 J04080 C1S Complement component 1, s subcomponent X76029 Neuromedin U U14973 40S ribosomal protein S29 U24576 Breast tumor autoantigen L41066 NF-AT3 X60489 Elongation factor-1-beta M62843 Paraneoplastic encephalomyelitis antigen HUD HG662-HT662 Epstein-Barr Virus Small Rna-Associated Protein HG613-HT613 Ribosomal Protein S12 L42379 Quiescin (Q6) mRNA M13241 N-MYC U12404 HSPB1 Heat shock 27kD protein 1 M55998 Alpha-1 collagen type I gene S82240 RhoE U78027 L44L gene X06700 COL3A1 Alpha-1 type 3 collagen D13413 Tumor-associated 120 kDa nuclear protein p120 M74719 SEF2-1A protein (SEF2-1A) M93119 INSM1 Insulinoma-associated 1 M92287 CCND3 Cyclin D3 HG33-HT33 Ribosomal Protein S4 U16306 CSPG2 Chondroitin sulfate proteoglycan 2 Z37976 LTBP2 Latent transforming growth factor beta binding protein 2 X69150 Ribosomal protein S18 HG4542-HT4947 Ribosomal Protein L10 L41607 GCNT2 Glucosaminyl (N-acetyl) transferase 2 U43148 PTCH Patched homolog M30269 NID Nidogen (enactin) X07384 GLI Glioma-associated oncogene homolog L38941 RPL37 Ribosomal protein L37 U09953 RPL9 Ribosomal protein L9 D87464 KIAA0274 gene M18000 40S ribosomal protein S17 M91196 ICSBP1 Interferon consensus sequence binding protein 1 L27559 IGFBP5 Insulin-like growth factor binding protein 5 S76475 NTRK3 Neurotrophic tyrosine kinase, receptor, type 3 (TrkC) L41067 Transcription factor NFATx -3s -2s -1s 0 +1s +2s +3s s = standard deviation from mean N-MYC PTCH GLI

4. 2B

5. 3A Overall Survival 0 .2 .4 .6 .8 1 3B p-val=0.0000033 0 20 40 60 80 100 120 Failures Survivors Months C1 C0 C1 C0 Markers of Survival L06419 PLOD Lysyl hydroxylase J02611 APOD Apolipoprotein D D86974 KIAA0220 gene U37673 Beta-NAP U28963 Gps2 (GPS2) X69636 H.sapiens mRNA sequence (15q11-13) U18018 ETV4 Ets variant gene 4 (E1A enhancer-binding protein, E1AF) M97287 SATB1 Special AT-rich sequence binding protein 1 U78180 Sodium channel 2 (hBNaC2) mRNA, alternatively spliced S76475 NTRK3 Neurotrophic tyrosine kinase, receptor, type 3 (TrkC) D28124 Unknown product U70867 Prostaglandin transporter hPGT M17733 Thymosin beta-4 L10333 Neuroendocrine-specific protein A (NSP) D14686 AMT Glycine cleavage system protein T (aminomethyltransferase) S66541 B-50 neural phosphoprotein AC002045 A-589H1.2 from Homo sapiens Chromosome 16 BAC clone CIT987-SKA-589H1 M96739 NSCL-1 D86963 PTB Ribosomal protein L26 U40271 PTK7 Protein-tyrosine kinase 7 L09229 FACL1 Long chain fatty acid acyl-coA ligase D78012 CRMP1 Collapsin response mediator protein 1 M74715 IDUA Iduronidase, alpha-L- HG2525-HT2621 Helix-Loop-Helix Protein Delta Max, Alt. Splice 1 L32164 Zinc finger protein L04731 Translocation T(4:11) of ALL-1 gene to chromosome 4 M22919 MLC gene (non-muscle myosin light chain) X15882 COL6A2 Collagen, type VI, alpha 2 U20657 Ubiquitin protease (Unph) proto-oncogene L17327 Pre-T/NK cell associated protein (3B3) J05412 REG1A Regenerating islet-derived 1 alpha (pancreatic stone protein) D43682 Very-long-chain acyl-CoA dehydrogenase (VLCAD) X58521 Nuclear pore glycoprotein P62 M21142 Guanine nucleotide-binding protein G-s-alpha-3 gene X52896 RNA for dermal fibroblast elastin D50663 CW-1 U35139 NECDIN related protein U16660 Peroxisomal enoyl-CoA hydratase-like protein (HPXEL) U04241 Homolog of Drosophila enhancer of split m9/m10 Y07847 RRP22 protein U78521 Immunophilin homolog ARA9 X93511 Telomeric repeat binding factor (TRF1) D30715 Exon2a from Human PAP (pancreatitis-associated protein) gene U51920 SRP54 Signal recognition particle 54 kD protein U02619 TFIIIC Box B-binding subunit U14417 Ral guanine nucleotide dissociation stimulator M73547 Human polyposis locus (DP1 gene) U09820 Helicase II (RAD54L) X13461 Calmodulin-related protein NB-1 Z56281 Interferon regulatory factor 3 Markers of Treatment Failure X69150 Ribosomal protein S18 M36072 RPL7A Ribosomal protein L7a X13293 MYBL2 V-myb avian myeloblastosis viral oncogene homolog-like 2 U14972 Ribosomal protein S10 K03189 Chorionic gonadotropin (hcg) beta subunit L17131 High mobility group protein (HMG-I(Y)) X13482 Human mRNA for U2 snRNP-specific A' protein L12711 TKT Transketolase L19711 Dystroglycan (DAG1) X04741 U2 small nuclear ribonucleoprotein A’ U12404 HSPB1 Heat shock 27kD protein 1 U15008 SnRNP core protein Sm D2 U81375 Placental equilibrative nucleoside transporter 1 (hENT1) X13794 Lactate dehydrogenase B gene Z49148 Enhancer of rudimentary homolog U39318 AF-4 X67247 RpS8 gene for ribosomal protein S8 U14968 Ribosomal protein L27a HG613-HT613 Ribosomal Protein S12 D63880 KIAA0159 gene Y07604 Nucleoside-diphosphate kinase J04823 Cytochrome c oxidase subunit VIII (COX8) M13934 RPS14 gene U30872 CENP-F kinetochore protein M81757 40S ribosomal protein S19 L07515 Human heterochromatin protein homologue (HP1) M14328 ENO1 Enolase 1, (alpha) D82348 5-aminoimidazole-4-carboxamide-1-beta-D-ribonucleoti de transformylase/inosinicase D78586 Human CAD mRNA for multifunctional protein CAD M32886 SRI Sorcin U31556 E2F5 E2F transcription factor 5, p130-binding X94910 ERp31 protein Y10313 Nerve growth factor-inducible PC4 homologue S78187 M-phase inducer phosphatase 2 HG2479-HT2575 Helix-Loop-Helix Protein Sef2-1d U12595 Tumor necrosis factor type 1 receptor associated protein (TRAP1) L36720 Bystin HG3214-HT3391 Metallopanstimulin 1 HG4542-HT4947 Ribosomal Protein L10 D29805 GGTB2 Glycoprotein-4-beta-galactosyltransferase 2 X52966 RPL35A Ribosomal protein L35a M64716 RPS25 Ribosomal protein S25 M64347 FGFR3 Fibroblast growth factor receptor 3 U09770 Cysteine-rich heart protein (hCRHP) D28473 IARS Isoleucine-tRNA synthetase X69908 P2 gene for c subunit of mitochondrial ATP synthase gene U76638 BRCA1-associated RING domain protein (BARD1) X79234 Ribosomal protein L11 X15376 GABRG2 Gamma-aminobutyric acid (GABA) A receptor, gamma 2 M14199 LAMR1 Laminin receptor (2H5 epitope) -3s -2s -1s 0 +1s +2s +3s s = standard deviation from mean